LAMMPS (9 Oct 2020)
  using 1 OpenMP thread(s) per MPI task
# Rhodopsin model

units           real
neighbor	2.0 bin
neigh_modify    delay 5 every 1

atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
pair_style      lj/charmm/coul/long 8.0 10.0
pair_modify     mix arithmetic
kspace_style    pppm 1e-4

read_data       data.protein
Reading data file ...
  orthogonal box = (-27.500000 -38.500000 -36.364600) to (27.500000 38.500000 36.361500)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  32000 atoms
  reading velocities ...
  32000 velocities
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  8 = max angles/atom
  scanning dihedrals ...
  18 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  reading bonds ...
  27723 bonds
  reading angles ...
  40467 angles
  reading dihedrals ...
  56829 dihedrals
  reading impropers ...
  1034 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0.0      0.0      0.0     
  special bond factors coul:  0.0      0.0      0.0     
     4 = max # of 1-2 neighbors
    12 = max # of 1-3 neighbors
    24 = max # of 1-4 neighbors
    26 = max # of special neighbors
  special bonds CPU = 0.005 seconds
  read_data CPU = 0.210 seconds

fix             1 all shake 0.0001 5 0 m 1.0 a 232
    1617 = # of size 2 clusters
    3633 = # of size 3 clusters
     747 = # of size 4 clusters
    4233 = # of frozen angles
  find clusters CPU = 0.003 seconds
fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1

special_bonds   charmm

thermo_style    multi
timestep        2.0

run		100
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
  G vector (1/distance) = 0.24883488
  grid = 25 32 32
  stencil order = 5
  estimated absolute RMS force accuracy = 0.035547797
  estimated relative force accuracy = 0.00010705113
  using double precision KISS FFT
  3d grid and FFT values/proc = 13230 6400
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 10 13 13
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 49.25 | 49.35 | 49.64 Mbytes
---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -149.3301 
Volume   =    307995.0335 
---------------- Step      100 ----- CPU =      5.5375 (sec) ----------------
TotEng   =    -25290.7303 KinEng   =     21591.9085 Temp     =       301.0906 
PotEng   =    -46882.6388 E_bond   =      2567.9807 E_angle  =     10781.9571 
E_dihed  =      5198.7492 E_impro  =       216.7864 E_vdwl   =     -1902.6618 
E_coul   =    206659.5225 E_long   =   -270404.9730 Press    =         6.7406 
Volume   =    308134.2285 
Loop time of 5.53765 on 4 procs for 100 steps with 32000 atoms

Performance: 3.120 ns/day, 7.691 hours/ns, 18.058 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.8921     | 3.9427     | 4.0762     |   3.9 | 71.20
Bond    | 0.16218    | 0.16829    | 0.17972    |   1.7 |  3.04
Kspace  | 0.35196    | 0.48475    | 0.53996    |  11.1 |  8.75
Neigh   | 0.69975    | 0.69981    | 0.69988    |   0.0 | 12.64
Comm    | 0.04908    | 0.049445   | 0.049767   |   0.1 |  0.89
Output  | 5.1737e-05 | 8.5056e-05 | 0.00018382 |   0.0 |  0.00
Modify  | 0.18393    | 0.18474    | 0.18528    |   0.1 |  3.34
Other   |            | 0.007858   |            |       |  0.14

Nlocal:        8000.00 ave        8143 max        7933 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost:        22733.5 ave       22769 max       22693 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs:    3.00702e+06 ave  3.0975e+06 max 2.96492e+06 min
Histogram: 1 2 0 0 0 0 0 0 0 1

Total # of neighbors = 12028093
Ave neighs/atom = 375.87791
Ave special neighs/atom = 7.4318750
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:05
